The Impact of Nucleotide Modifications on the Immune Responses of mRNA Vaccines

Messenger RNA (mRNA) vaccines play an important role in preventing infections and treating cancer. They offer notable advantages, including rapid design, flexible antigen encoding, and the feasibility of large-scale production. Despite these benefits, mRNA vaccines face some challenges, such as unintended immune activation, poor stability, and limited protein yield. Chemical modifications can help overcome these problems. Examples include N1-methylpseudouridine, 2’-O-methylation, and 5-methylcytidine. These changes improve stability and reduce immunogenicity. In addition, adjusting the 5' cap, controlling poly(A) tail length, and modifying untranslated regions (UTRs) can increase protein production and extend mRNA lifespan in the body. Together, these improvements increase antigen production, also strengthen immune responses against viruses, tumors, and chronic infections such as hepatitis B. Some challenges remain, like we need to know how modifications affect translation accuracy, how cells need different poly(A) lengths and UTRs, and how to combine cap changes with large-scale production. Addressing these problems is important to achieve safer and more effective mRNA therapies. This review summarizes current knowledge on nucleotide changes and design rules. It explains how they influence stability, translation efficiency, and immune activation, and offers advice on making the next generation of mRNA vaccines safer and more effective in clinical use.